An analysis of large rRNA sequences folded by a thermodynamic method - PubMed (original) (raw)
An analysis of large rRNA sequences folded by a thermodynamic method
D S Fields et al. Fold Des. 1996.
Abstract
Background: The secondary structure of RNA can be predicted by the thermodynamics-based method of Zuker and Turner. The accuracy of the method's secondary structure predictions for rRNA can be assessed by using as reference the currently available rRNA secondary structure models that have been derived from comparative analysis of rRNA sequence alignments.
Results: We folded 72 23S rRNA sequences with the Zuker-Turner method and scored the resulting secondary structure predictions against the comparative model. Empirically, trends in the score were observed as a function of the phylogenetic memberships of the sequences and as a function of the base pairs secondary structural contexts. Further, three parameters were found that (anti-)correlate with the score.
Conclusions: Three semiquantitative predictors of score were found: % of noncanonical base pairs, % of hairpin loops that were stable tetraloops, and sequence %G + C. The folding of rRNA is a tractable problem and thermodynamics-based folding algorithms, in particular, are useful in the study of this folding problem even for large RNA molecules (e.g. 16S and 23S rRNA).
Similar articles
- Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.
Leontis NB, Stombaugh J, Westhof E. Leontis NB, et al. Biochimie. 2002 Sep;84(9):961-73. doi: 10.1016/s0300-9084(02)01463-3. Biochimie. 2002. PMID: 12458088 - Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package.
Kumar Y, Westram R, Kipfer P, Meier H, Ludwig W. Kumar Y, et al. BMC Bioinformatics. 2006 May 4;7:240. doi: 10.1186/1471-2105-7-240. BMC Bioinformatics. 2006. PMID: 16672074 Free PMC article. - RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing.
Tang TH, Rozhdestvensky TS, d'Orval BC, Bortolin ML, Huber H, Charpentier B, Branlant C, Bachellerie JP, Brosius J, Hüttenhofer A. Tang TH, et al. Nucleic Acids Res. 2002 Feb 15;30(4):921-30. doi: 10.1093/nar/30.4.921. Nucleic Acids Res. 2002. PMID: 11842103 Free PMC article. - A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs.
Konings DA, Gutell RR. Konings DA, et al. RNA. 1995 Aug;1(6):559-74. RNA. 1995. PMID: 7489516 Free PMC article. - The accuracy of ribosomal RNA comparative structure models.
Gutell RR, Lee JC, Cannone JJ. Gutell RR, et al. Curr Opin Struct Biol. 2002 Jun;12(3):301-10. doi: 10.1016/s0959-440x(02)00339-1. Curr Opin Struct Biol. 2002. PMID: 12127448 Review.
Cited by
- Thirteen dubious ways to detect conserved structural RNAs.
Gao W, Yang A, Rivas E. Gao W, et al. IUBMB Life. 2023 Jun;75(6):471-492. doi: 10.1002/iub.2694. Epub 2022 Dec 10. IUBMB Life. 2023. PMID: 36495545 Free PMC article. - MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome.
Rorbach J, Boesch P, Gammage PA, Nicholls TJ, Pearce SF, Patel D, Hauser A, Perocchi F, Minczuk M. Rorbach J, et al. Mol Biol Cell. 2014 Sep 1;25(17):2542-55. doi: 10.1091/mbc.E14-01-0014. Epub 2014 Jul 9. Mol Biol Cell. 2014. PMID: 25009282 Free PMC article. - Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes.
van der Sluis EO, Bauerschmitt H, Becker T, Mielke T, Frauenfeld J, Berninghausen O, Neupert W, Herrmann JM, Beckmann R. van der Sluis EO, et al. Genome Biol Evol. 2015 Apr 9;7(5):1235-51. doi: 10.1093/gbe/evv061. Genome Biol Evol. 2015. PMID: 25861818 Free PMC article. - The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. Cannone JJ, et al. BMC Bioinformatics. 2002;3:2. doi: 10.1186/1471-2105-3-2. Epub 2002 Jan 17. BMC Bioinformatics. 2002. PMID: 11869452 Free PMC article. - Structures of the human and Drosophila 80S ribosome.
Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN, Beckmann R. Anger AM, et al. Nature. 2013 May 2;497(7447):80-5. doi: 10.1038/nature12104. Nature. 2013. PMID: 23636399